To measure discrepancies in risk adjustment scores using only Medicaid or Veterans Health Administration (VA) diagnoses for Veterans dually enrolled in VA and Medicaid. Veterans aged 18-64 enrolled in the VA and Medicaid for at least one full calendar year during 2017-2020. We compared the number and overlap of annual diagnoses derived from VA and Medicaid data. We also calculated Charlson, Elixhauser, and Centers for Medicare and Medicaid Hierarchical Condition Categories Version 21 (CMS-V21) risk scores using VA-only, Medicaid-only, and combined VA-Medicaid data for each person-year. We used intraclass correlations within risk measures to compare scores across risk measures. Our study cohort contained 183,018 dual-enrollees with service-connected disabilities representing 405,318 person years and 219,977 dual enrollees without service-connected disabilities (531,948 person years). On average, service-connected individuals had 9.1 fewer diagnoses from Medicaid-only data than from VA-only data (95% CI, 9.0-9.1) and 5.0 fewer for non-service-connected Veterans (95% CI, 4.9-5.1). Intraclass correlations between VA-only data and combined VA-Medicaid scores had higher correlations for Charlson and Elixhauser scores, while Medicaid-only scores had higher correlations for CMS V21. Medicaid and VA data represent non-overlapping diagnoses data in three common risk scores. Researchers should consider combining records to calculate disease burden for dual-enrolled Veterans to ensure complete capture of risk.